MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. Academic Article uri icon


  • Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-throughput computational analysis, as well as AMR++, a customized bioinformatic pipeline specifically designed to use MEGARes in high-throughput analysis for characterizing AMR genes (ARGs) in metagenomic sequence data. Here, we present MEGARes v3.0, a comprehensive database of published ARG sequences for antimicrobial drugs, biocides, and metals, and AMR++ v3.0, an update to our customized bioinformatic pipeline for high-throughput analysis of metagenomic data (available at Database annotations have been expanded to include information regarding specific genomic locations for single-nucleotide polymorphisms (SNPs) and insertions and/or deletions (indels) when required by specific ARGs for resistance expression, and the updated AMR++ pipeline uses this information to check for presence of resistance-conferring genetic variants in metagenomic sequenced reads. This new information encompasses 337 ARGs, whose resistance-conferring variants could not previously be confirmed in such a manner. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include 4 antimicrobial compound types, 59 resistance classes, 233 mechanismsand 1448 gene groups that classify the 8733 accessions.

published proceedings

  • Nucleic Acids Res

altmetric score

  • 16.9

author list (cited authors)

  • Bonin, N., Doster, E., Worley, H., Pinnell, L. J., Bravo, J. E., Ferm, P., ... Boucher, C.

citation count

  • 3

complete list of authors

  • Bonin, Nathalie||Doster, Enrique||Worley, Hannah||Pinnell, Lee J||Bravo, Jonathan E||Ferm, Peter||Marini, Simone||Prosperi, Mattia||Noyes, Noelle||Morley, Paul S||Boucher, Christina

publication date

  • January 2023